diff --git a/CHANGELOG.md b/CHANGELOG.md index b717ea18..06538dd2 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,6 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Add `apple` profile to enable the use of Apple containers. - Drop `hook_url` parameter. To configure messaging services, use a custom config in tandem with the `nf-teams`/`nf-slack` plugin instead. - Drop `run_coverage` and add `qc_mode` parameter. Thorough coveage analysis is now included in the `qc_mode` parameter, which can be set to `basic` or `full`. Basic QC includes samtools flagstat, idxstats and mosdepth. Full QC includes samtools stats, samtools coverage, riker metrics and panel coverage in addition to basic QC. +- Revert the default configs base to the nf-core configs in preparation of converting nf-cmgg/configs to a private repo ## 3.0.2 diff --git a/conf/test.config b/conf/test.config index 0feb22b8..5bc96734 100644 --- a/conf/test.config +++ b/conf/test.config @@ -16,7 +16,6 @@ params { // Input data input = "${projectDir}/tests/inputs/test.yml" - custom_config_base = null } process { diff --git a/main.nf b/main.nf index 55cf77de..a38a7b3a 100644 --- a/main.nf +++ b/main.nf @@ -44,24 +44,6 @@ params { // Directory containing gene list bed files for granular coverage analysis genelists: Path? - // Git commit id for Institutional configs. - custom_config_version: String = 'main' - - // Base directory for custom configs. - custom_config_base: String = 'https://raw.githubusercontent.com/nf-cmgg/configs/main' - - // Institutional config name. - config_profile_name: String? - - // Institutional config description. - config_profile_description: String? - - // Institutional config contact information. - config_profile_contact: String? - - // Institutional config URL link. - config_profile_url: String? - // Display version and exit. version: Boolean = false diff --git a/nextflow.config b/nextflow.config index ce437d8b..db21863a 100644 --- a/nextflow.config +++ b/nextflow.config @@ -16,8 +16,8 @@ params { pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/' trace_report_suffix = new java.util.Date().format('yyyy-MM-dd_HH-mm-ss') - custom_config_version = 'main' - custom_config_base = "https://raw.githubusercontent.com/nf-cmgg/configs/${params.custom_config_version}" + custom_config_version = 'master' + custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}" outdir = './results' } diff --git a/nextflow_schema.json b/nextflow_schema.json index 55ee6080..21cfec2b 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -86,14 +86,14 @@ "custom_config_version": { "type": "string", "description": "Git commit id for Institutional configs.", - "default": "main", + "default": "master", "hidden": true, "fa_icon": "fas fa-users-cog" }, "custom_config_base": { "type": "string", "description": "Base directory for custom configs.", - "default": "https://raw.githubusercontent.com/nf-cmgg/configs/main", + "default": "https://raw.githubusercontent.com/nf-core/configs/master", "hidden": true, "help_text": "If you're running offline, Nextflow will not be able to fetch the custom config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.", "fa_icon": "fas fa-users-cog"